Interpretive Summary: Theobroma cacao or cacao is a tropical tree that produces the raw material used to make chocolate. Misidentified cacao trees in germplasm collections hinder the development of new cultivars. Furthermore, crossing closely related cacao trees can result in lower yields in the offspring. In this study the ancestry of the two cacao populations (ICS and TRD) from Trinidad were studied. The information in this study facilitates the development of productive cacao hybrids. The data presented will assist germplasm curators to make informed decisions and will benefit plant breeders, extension workers and ultimately cacao producers.

Technical Abstract:
Population structure of the original Trinitario cacao in Trinidad was evaluated from the 35 microsatellite multi-loci profile of 32 TRD (relic clones from abandoned cacao estates in Trinidad) and 88 ICS clones conserved in the International Cocoa Genebank, Trinidad (ICGT). Ancestry was derived by comparison to 34 representative genotypes of Criollo, Central American, Lower and Upper Amazon origin. The 154 individuals separated into four populations labeled population 1 -Upper Amazon, population 2 - Ecuadorian, population 3- Lower Amazon and population 4-Trinitario in this study. Over 90% of the individuals demonstrated 70% to 99% membership to their respective populations. The ICS and TRD clones formed a genetically homogenous group, 84% of which clustered in population 4 with clones of pure Criollo descent. Another 10% clustered in population 1 containing clones of Upper Amazon descent. The cacao population of Trinidad is genetically different from clones in population 2 of Ecuadorian descent and was completely unrelated to the clones in population 3. The level of genetic redundancy was 28% among the TRD and ICS clones with 12 full-sib families identified. The level of duplicated genotypes was 5% with mislabeled and misidentified clones being discovered. Polymorphism information content (PIC) values of each of the 35 microsatellite loci among populations showed that the 10 most discriminating loci for each population were different. This is the first report to provide a strong genetic basis for the industry flavor distinction of Trinitario and Ecuadorian cacaos. Curator-ship of cacao collections and maintenance of flavor classes are discussed in relation to breeding for disease resistance in cacao.